pct_reads_mapped

metrics.pct_reads_mapped(mqc, biosample_id)

Description: The percentage of short paired-end sequencing high quality reads, primary alignments, mapped on GRCh38 assembly. Duplicated reads and clipped bases are included. No minimum mapping quality is imposed.

Implementation details: In the NPM-sample-QC reference implementation it is computed using samtools stats, reporting the percentage of reads mapped on GRCh38 assembly. Duplicated reads are included. No mapping qualiy is applied.